Required Packages and functions

# libraries
library(sas7bdat)
library(sva)
library(reshape)
library(ggplot2)
library(gridExtra)
library(knitr)
library(dplyr)
library(kableExtra)
library(tidyverse)
library(minfi)
library(stringr)
library(limma)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(minfi)
library(DMRcate)
library(UpSetR)
library(reshape)
library(corrplot)
library(factoextra)
library(ENmix)

# loading annotation
anno = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)
anno = data.frame(anno)

# loading functions
setwd('/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local')
source('EWAS functions.R')

Load DNAm and pheno data

load("/Users/annebozack/Box/NIEHS-R01 ONES/Methylation Data/Age7Blood_ComBat_Betas_Mvals_filteredProbes_metalAnalaysis.RData")

dim(pDatAge7Metal)
# 333 164

dim(ComBat.Mvalues.Metals)
# 394460    333

rownames(pDatAge7Metal) = pDatAge7Metal$samplename

pDatAge7Metal$age_yrs_7y_blood = pDatAge7Metal$c_age_days_7y_blood/365

# smoking 
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'xnever'] = 0
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'former'] = 1
pDatAge7Metal$smk_preg2[pDatAge7Metal$smokpreg_final_d == 'smoke preg'] = 2
pDatAge7Metal$smk_preg2 = factor(pDatAge7Metal$smk_preg2)

EWAS

As

DMP_As_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk')
 
# Unadjusted, N =  333 
# Unadjusted, p<0.05:  23361 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15990 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9130156 
 
# Number of DMRs identified:   5 

DMP_As_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
2 113992761 113993313 0 552 0 0.00e+00 8
3 46759437 46759698 0 261 0 8.00e-07 7
1 228395659 228396009 0 350 0 7.00e-07 5
17 1395863 1396123 0 260 0 2.00e-06 5
17 75315485 75315667 0 182 0 2.62e-05 6

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_manhattan_DMP_adj.png")

As, female

pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))

DMP_As_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26064 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16222 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9159963 

# Number of DMRs identified:   4 

DMP_As_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
7 76027000 76027101 0.0e+00 101 0.0e+00 0.0000017 3
1 11561496 11561711 0.0e+00 215 0.0e+00 0.0000058 3
2 113992842 113993142 0.0e+00 300 0.0e+00 0.0000341 5
2 198651075 198651347 8.8e-06 272 8.8e-06 0.0127295 3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_manhattan_DMP_adj.png")

As, male

pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))

DMP_As_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  11497 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13972 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8382292 
 
# Number of DMRs identified:   4 

DMP_As_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
17 47091977 47092178 0e+00 201 0e+00 0.0000001 4
8 22735275 22735478 0e+00 203 1e-07 0.0000619 4
2 164204751 164205032 1e-07 281 1e-07 0.0001212 4
16 88706240 88706389 8e-07 149 8e-07 0.0021312 2

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_manhattan_DMP_adj.png")

Ba

DMP_Ba_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk')

Unadjusted, N =  333 
Unadjusted, p<0.05:  11801 
Unadjusted, FDR<0.05:  0 
Unadjusted, pBonf<0.05:  0 
 
Adjusted, N =  333 
Adjusted, p<0.05:  12058 
Adjusted, FDR<0.05:  0 
Adjusted, pBonf<0.05:  0 
Adjusted, lambda:  0.7933736 
 
Number of DMRs identified:   3 

DMP_Ba_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
17 6899084 6899577 0 493 0 0.0e+00 10
6 32145349 32145923 0 574 0 4.0e-07 20
16 1583809 1584118 0 309 0 4.6e-06 6
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, female

DMP_Ba_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  29651 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  23980 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.210756 
 
# Number of DMRs identified:   6

DMP_Ba_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
17 6899084 6899577 0.0000000 493 0.0000000 0.0000000 10
17 37123637 37123949 0.0000000 312 0.0000000 0.0000011 9
22 30476088 30476345 0.0000000 257 0.0000001 0.0000450 8
2 183943387 183943551 0.0000000 164 0.0000001 0.0000863 5
8 144635308 144635610 0.0000005 302 0.0000005 0.0005899 8
7 94285269 94285288 0.0011747 19 0.0011747 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, male

DMP_Ba_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  25363 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  25117 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.190464 
 
# Number of DMRs identified:   3 

DMP_Ba_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
16 1583809 1584118 0e+00 309 0e+00 0.0000000 6
19 50194119 50194252 0e+00 133 0e+00 0.0000061 5
6 29595001 29595335 1e-07 334 1e-07 0.0001585 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_manhattan_DMP_adj.png")

Cd

DMP_Cd_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  9428 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  11898 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.8219919 
 
# Number of DMRs identified:   3 

DMP_Cd_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg07044523 0.26 (0.17 ,0.34) 5.28 0 0.0021538 0.0022 chr1 153514376 S100A5

DMRs

chr start end p length fdr sidak nprobe
7 158045979 158046166 0 187 0 6.7e-06 3
5 23507449 23507656 0 207 0 9.6e-06 5
17 46685291 46685448 0 157 0 5.6e-05 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, female

DMP_Cd_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  13276 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  13415 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8339903 
 
# Number of DMRs identified:   6

DMP_Cd_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
6 32164926 32165321 0.0000000 395 0.0000000 0.0000000 7
17 46685291 46685448 0.0000000 157 0.0000000 0.0000008 5
6 1624385 1624442 0.0000001 57 0.0000001 0.0003821 2
5 23507449 23507656 0.0000001 207 0.0000001 0.0001196 5
11 73357094 73357276 0.0000020 182 0.0000025 0.0044181 6
5 132113754 132113860 0.0179428 106 0.0179428 1.0000000 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, male

DMP_Cd_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16666 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  21565 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.111181 
 
# Number of DMRs identified:   3 

# DMP_Cd_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
20 61446961 61447369 0.00e+00 408 0.00e+00 0.0000000 11
7 50518572 50518647 1.80e-06 75 2.80e-06 0.0096276 2
6 28446839 28447087 6.28e-05 248 6.28e-05 0.0951117 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_manhattan_DMP_adj.png")

Cr

DMP_Cr_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk')

# # Unadjusted, N =  333 
# Unadjusted, p<0.05:  29723 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23609 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.115003 
 
# Number of DMRs identified:   5 

DMP_Cr_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
5 145758709 145758881 0.00e+00 172 0.00e+00 0.0000182 4
16 66969473 66969500 0.00e+00 27 1.00e-07 0.0003708 2
6 33245769 33245990 7.00e-07 221 1.10e-06 0.0012157 7
19 50666378 50666538 2.37e-05 160 2.74e-05 0.0567867 3
6 33280198 33280228 2.74e-05 30 2.74e-05 0.3024815 3

No adjustment for fish consumption

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, female

DMP_Cr_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26701 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  24909 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.186951 
 
# Number of identified DMR:  0

DMP_Cr_F_age7[[3]] = NULL
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, male

DMP_Cr_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  17887 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  12574 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8769853 
 
# Number of DMRs identified:   1

DMP_Cr_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
17 46685291 46685448 0 157 0 1.8e-06 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_manhattan_DMP_adj.png")

Cs

DMP_Cs_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  16687 
# Unadjusted, FDR<0.05:  4 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  13318 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8387198 
 
# Number of DMRs identified:   5 

DMP_Cs_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
13 47472049 47472429 0.0000000 380 0.0000001 0.0000226 12
6 33280051 33280228 0.0000000 177 0.0000001 0.0000553 6
10 94820922 94821085 0.0000001 163 0.0000001 0.0001480 6
6 32847761 32847845 0.0000449 84 0.0000561 0.1900047 7
20 57427641 57427762 0.0010524 121 0.0010524 0.9677029 6
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, female

DMP_Cs_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  25871 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16348 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9656277 
 
# Number of DMRs identified:   3 

DMP_Cs_F_age7[[3]]= NULL

DMRs

chr start end p length fdr sidak nprobe
1 200272111 200272215 0 104 0 2.10e-05 3
20 3145355 3145597 0 242 0 1.32e-05 3
6 29648378 29648628 0 250 0 3.89e-05 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, male

DMP_Cs_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk')

Unadjusted, N =  175 
Unadjusted, p<0.05:  15896 
Unadjusted, FDR<0.05:  0 
Unadjusted, pBonf<0.05:  0 
 
Adjusted, N =  175 
Adjusted, p<0.05:  15716 
Adjusted, FDR<0.05:  0 
Adjusted, pBonf<0.05:  0 
Adjusted, lambda:  0.9276189 
 
Number of DMRs identified:   1 
 
DMP_Cs_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
20 57427555 57427762 1.86e-05 207 1.86e-05 0.0347322 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_manhattan_DMP_adj.png")

Cu

DMP_Cu_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  10199 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20001 
# Adjusted, FDR<0.05:  29 
# Adjusted, pBonf<0.05:  8 
# Adjusted, lambda:  1.082819 

# Number of DMRs identified:   18 

DMP_Cu_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00082497 -0.25 (-0.36 ,-0.15) -5.32 2.8e-06 0.0375331 1.0000 chr1 32802133 MARCKSL1
cg00116766 0.42 (0.28 ,0.56) 2.04 0.0e+00 0.0013289 0.0021 chr16 9857614 GRIN2A;GRIN2A;GRIN2A
cg00908120 0.52 (0.33 ,0.7) 6.26 1.0e-07 0.0056610 0.0509 chr16 72872925 ZFHX3;ZFHX3
cg02155957 0.38 (0.23 ,0.53) 3.25 7.0e-07 0.0150267 0.2705 chr1 46930731
cg04015129 0.7 (0.44 ,0.96) 4.28 3.0e-07 0.0080222 0.1043 chr10 1058036 GTPBP4
cg04692924 -0.42 (-0.59 ,-0.26) -6.61 1.0e-06 0.0191351 0.4018 chr1 161720042 DUSP12
cg05051957 -0.45 (-0.63 ,-0.28) -5.60 4.0e-07 0.0105360 0.1686 chr8 141522459 CHRAC1;CHRAC1
cg05955013 -0.4 (-0.55 ,-0.24) -6.28 4.0e-07 0.0105360 0.1624 chr17 45056646 RPRML
cg06723863 -0.26 (-0.36 ,-0.15) -5.98 1.8e-06 0.0275171 0.7154 chr16 68270129 ESRP2;ESRP2
cg07380021 -0.51 (-0.69 ,-0.32) -5.42 1.0e-07 0.0056342 0.0451 chr1 206755252 RASSF5;RASSF5;RASSF5
cg07831553 0.61 (0.36 ,0.86) 3.37 2.5e-06 0.0358634 1.0000 chr19 48796974
cg08370347 0.51 (0.3 ,0.72) 3.91 1.7e-06 0.0266105 0.6653 chr5 171571793 STK10
cg10145926 0.61 (0.39 ,0.84) 5.31 2.0e-07 0.0061658 0.0678 chr14 95875792 C14orf139
cg10653573 0.82 (0.49 ,1.15) 5.43 1.4e-06 0.0251851 0.5541 chr8 141347297 TRAPPC9;TRAPPC9
cg10923018 0.24 (0.16 ,0.32) 2.75 0.0e+00 0.0026797 0.0134 chr6 31743769 C6orf27
cg11608893 0.61 (0.36 ,0.86) 6.05 1.6e-06 0.0266105 0.6420 chr6 32059542 TNXB
cg12067421 -0.46 (-0.62 ,-0.31) 2.01 0.0e+00 0.0015700 0.0047 chr1 203246482
cg13434714 -0.42 (-0.58 ,-0.26) -5.77 8.0e-07 0.0172634 0.3280 chr12 6936787 LEPREL2
cg15790767 1.05 (0.67 ,1.42) 3.84 1.0e-07 0.0042467 0.0297 chr6 13431216 GFOD1
cg17143270 0.82 (0.51 ,1.14) 5.74 4.0e-07 0.0105360 0.1677 chr1 91532819
cg18299835 -0.23 (-0.33 ,-0.14) -4.13 2.1e-06 0.0304573 0.8223 chr19 13207445 NFIX
cg18714712 -0.54 (-0.72 ,-0.36) -5.97 0.0e+00 0.0013289 0.0027 chr19 49866917 DKKL1;TEAD2
cg19532212 0.49 (0.31 ,0.67) 4.46 3.0e-07 0.0080222 0.1016 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C
cg19842134 -0.29 (-0.4 ,-0.17) -3.53 9.0e-07 0.0178044 0.3561 chr12 54070591 ATP5G2;ATP5G2
cg20365618 -0.24 (-0.34 ,-0.15) 0.42 1.5e-06 0.0262342 0.6034 chr10 121578384 INPP5F;INPP5F
cg23477849 0.28 (0.19 ,0.38) 4.88 0.0e+00 0.0020266 0.0081 chr19 5698492 LONP1
cg25954729 -0.22 (-0.3 ,-0.14) -6.34 2.0e-07 0.0059844 0.0598 chr11 66610784 RCE1;C11orf80;RCE1
cg26708724 0.66 (0.41 ,0.92) 6.73 5.0e-07 0.0120529 0.2049 chr4 187509785 FAT1
cg27565067 0.48 (0.31 ,0.65) 6.20 0.0e+00 0.0029493 0.0177 chr17 149484 RPH3AL

DMRs

chr start end p length fdr sidak nprobe
22 45704901 45705265 0.0e+00 364 0.0e+00 0.0000000 7
20 35169538 35169886 0.0e+00 348 0.0e+00 0.0000000 6
16 66304366 66304585 0.0e+00 219 0.0e+00 0.0000001 3
10 121578136 121578639 0.0e+00 503 0.0e+00 0.0000001 4
12 54070516 54070610 0.0e+00 94 0.0e+00 0.0000006 5
16 8806530 8806756 0.0e+00 226 0.0e+00 0.0000004 7
17 149483 149488 0.0e+00 5 0.0e+00 0.0001527 2
6 1604012 1604212 0.0e+00 200 0.0e+00 0.0000163 5
20 3052114 3052483 0.0e+00 369 0.0e+00 0.0000189 9
17 1395863 1396123 0.0e+00 260 0.0e+00 0.0000409 5
19 55660590 55660625 0.0e+00 35 0.0e+00 0.0003053 4
15 100048370 100048500 0.0e+00 130 1.0e-07 0.0001014 3
2 130345204 130345405 0.0e+00 201 1.0e-07 0.0000974 3
17 47091977 47092178 1.0e-07 201 1.0e-07 0.0001424 4
19 50194119 50194252 1.0e-07 133 1.0e-07 0.0002345 5
13 100310161 100310405 1.0e-07 244 1.0e-07 0.0001709 4
11 19736149 19736333 1.0e-07 184 1.0e-07 0.0002923 5
1 207082827 207082900 1.1e-06 73 1.1e-06 0.0059448 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, female

DMP_Cu_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  19233 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16152 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.952899 
 
# Number of DMRs identified:   11 

DMP_Cu_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
6 32063900 32064842 0.0000000 942 0.0000000 0.0000000 33
5 191295 191806 0.0000000 511 0.0000000 0.0000000 9
15 81426346 81426610 0.0000000 264 0.0000000 0.0000002 7
11 73357094 73357396 0.0000000 302 0.0000001 0.0000556 7
2 74875226 74875536 0.0000001 310 0.0000001 0.0000788 7
21 37442288 37442476 0.0000001 188 0.0000002 0.0002543 3
17 1395863 1396123 0.0000001 260 0.0000002 0.0001967 5
1 120174148 120174361 0.0000001 213 0.0000002 0.0002411 2
8 95962351 95962383 0.0000017 32 0.0000021 0.0210023 4
19 23941312 23941438 0.0001402 126 0.0001543 0.3553439 3
6 31734291 31734401 0.0007630 110 0.0007630 0.9352574 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, male

DMP_Cu_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  8255 
# Unadjusted, FDR<0.05:  32 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  11939 
# Adjusted, FDR<0.05:  49 
# Adjusted, pBonf<0.05:  14 
# Adjusted, lambda:  0.7284168 
 
# Number of DMRs identified:   14 

DMP_Cu_M_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00908120 0.71 (0.47 ,0.96) 6.29 1.0e-07 0.0017621 0.0229 chr16 72872925 ZFHX3;ZFHX3
cg01007589 0.91 (0.59 ,1.23) 4.79 1.0e-07 0.0030119 0.0422 chr19 49894178 CCDC155
cg01063965 -0.27 (-0.37 ,-0.17) -6.44 4.0e-07 0.0086883 0.1564 chr11 695461 TMEM80;TMEM80;DEAF1;DEAF1
cg01447660 0.39 (0.23 ,0.54) -0.92 1.9e-06 0.0224235 0.7624 chr2 69152678
cg01485439 0.51 (0.31 ,0.7) 3.65 7.0e-07 0.0130637 0.2613 chr11 67225937 CABP4
cg02155957 0.49 (0.29 ,0.68) 3.22 1.6e-06 0.0201772 0.6255 chr1 46930731
cg02196294 -0.26 (-0.37 ,-0.15) -5.41 4.2e-06 0.0349929 1.0000 chr6 39197260 KCNK5
cg02490920 0.37 (0.24 ,0.51) 1.34 3.0e-07 0.0075004 0.1275 chr3 50304406 SEMA3B;SEMA3B
cg02968175 0.31 (0.2 ,0.42) 5.76 2.0e-07 0.0053540 0.0857 chr16 4690020 MGRN1;MGRN1;MGRN1;MGRN1
cg03717239 0.3 (0.18 ,0.42) 0.51 2.7e-06 0.0271495 1.0000 chr8 145574318
cg03790745 0.28 (0.16 ,0.39) 5.56 3.5e-06 0.0321103 1.0000 chr11 63679432 RCOR2
cg04015129 0.85 (0.56 ,1.13) 4.27 0.0e+00 0.0010425 0.0090 chr10 1058036 GTPBP4
cg04406071 -0.3 (-0.41 ,-0.19) -6.07 5.0e-07 0.0096730 0.1838 chr17 59489784 C17orf82
cg04692924 -0.6 (-0.83 ,-0.37) -6.58 1.0e-06 0.0158267 0.3957 chr1 161720042 DUSP12
cg05051957 -0.62 (-0.86 ,-0.37) -5.61 1.3e-06 0.0178448 0.5175 chr8 141522459 CHRAC1;CHRAC1
cg05955013 -0.47 (-0.67 ,-0.28) -6.30 2.7e-06 0.0271495 1.0000 chr17 45056646 RPRML
cg07380021 -0.67 (-0.89 ,-0.45) -5.43 0.0e+00 0.0010425 0.0047 chr1 206755252 RASSF5;RASSF5;RASSF5
cg08329655 -0.44 (-0.6 ,-0.27) -5.88 1.1e-06 0.0163083 0.4470 chr11 7534677 PPFIBP2
cg08459368 0.58 (0.35 ,0.81) 2.70 1.7e-06 0.0203444 0.6510 chr11 61974948 SCGB2A1
cg08760128 0.31 (0.19 ,0.42) 6.73 9.0e-07 0.0155789 0.3739 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1
cg10266648 1.06 (0.69 ,1.43) 5.98 1.0e-07 0.0017511 0.0210 chr2 106560529
cg10923018 0.35 (0.24 ,0.46) 2.73 0.0e+00 0.0004255 0.0009 chr6 31743769 C6orf27
cg11608893 0.95 (0.64 ,1.26) 6.08 0.0e+00 0.0010425 0.0042 chr6 32059542 TNXB
cg12243007 0.46 (0.27 ,0.64) -0.77 3.3e-06 0.0310915 1.0000 chr17 184018 RPH3AL
cg13434714 -0.68 (-0.87 ,-0.48) -5.78 0.0e+00 0.0000612 0.0001 chr12 6936787 LEPREL2
cg13989834 0.55 (0.34 ,0.76) 3.14 9.0e-07 0.0146279 0.3364 chr9 134400392 UCK1;UCK1
cg15389183 -0.22 (-0.31 ,-0.13) -6.19 3.3e-06 0.0310915 1.0000 chr14 102829482 TECPR2;CINP
cg15790767 1.16 (0.68 ,1.64) 3.86 4.2e-06 0.0349929 1.0000 chr6 13431216 GFOD1
cg16068812 -1.01 (-1.42 ,-0.6) -4.27 2.5e-06 0.0271495 0.9973 chr21 44528396 U2AF1;U2AF1;U2AF1
cg16496814 0.28 (0.17 ,0.39) 5.22 1.1e-06 0.0163083 0.4461 chr11 9778721
cg16656826 0.33 (0.2 ,0.45) 0.14 7.0e-07 0.0135857 0.2853 chr5 159343871 ADRA1B;ADRA1B
cg18670846 0.73 (0.43 ,1.03) -2.30 3.7e-06 0.0324333 1.0000 chr2 68917482
cg18714712 -0.73 (-0.97 ,-0.48) -5.95 0.0e+00 0.0010425 0.0094 chr19 49866917 DKKL1;TEAD2
cg19005275 0.68 (0.45 ,0.92) 4.29 1.0e-07 0.0017511 0.0204 chr12 113588263 CCDC42B
cg19532212 0.7 (0.45 ,0.95) 4.42 2.0e-07 0.0051395 0.0771 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C
cg20365618 -0.35 (-0.47 ,-0.23) 0.40 0.0e+00 0.0010425 0.0063 chr10 121578384 INPP5F;INPP5F
cg20597842 0.99 (0.59 ,1.4) 5.88 3.1e-06 0.0308990 1.0000 chr12 7818585 APOBEC1
cg21373263 0.79 (0.48 ,1.09) 3.29 8.0e-07 0.0146279 0.3254 chr10 126751982 CTBP2;CTBP2
cg21864868 0.66 (0.4 ,0.91) 4.22 1.2e-06 0.0163083 0.4566 chr17 46673002 LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
cg22240394 1.07 (0.65 ,1.49) 6.82 1.4e-06 0.0183349 0.5500 chr3 186211630
cg22286640 -0.78 (-1.1 ,-0.46) -4.65 4.3e-06 0.0349929 1.0000 chr8 67026828
cg23312431 0.34 (0.2 ,0.47) -0.37 1.8e-06 0.0211836 0.6991 chr21 45773997 TRPM2
cg23477849 0.39 (0.25 ,0.52) 4.90 1.0e-07 0.0017511 0.0202 chr19 5698492 LONP1
cg24543538 0.84 (0.5 ,1.17) 3.22 2.0e-06 0.0228393 0.7994 chr2 241569846 GPR35
cg25514328 -0.47 (-0.66 ,-0.27) -4.77 3.6e-06 0.0321103 1.0000 chr17 78549324 RPTOR;RPTOR
cg25954729 -0.31 (-0.41 ,-0.21) -6.37 0.0e+00 0.0010425 0.0053 chr11 66610784 RCE1;C11orf80;RCE1
cg26543311 1.1 (0.64 ,1.56) 7.17 4.4e-06 0.0357043 1.0000 chr12 48875427 C12orf54
cg26708724 0.95 (0.63 ,1.27) 6.72 0.0e+00 0.0010425 0.0088 chr4 187509785 FAT1
cg27503275 0.43 (0.26 ,0.61) 4.12 2.7e-06 0.0271495 1.0000 chr6 3880016

DMRs

chr start end p length fdr sidak nprobe
10 121578136 121578846 0.0000000 710 0.0000000 0.0000000 5
22 45704901 45705265 0.0000000 364 0.0000000 0.0000000 7
21 45773781 45773997 0.0000000 216 0.0000000 0.0000009 2
4 24796918 24797176 0.0000000 258 0.0000000 0.0000093 6
19 50194119 50194252 0.0000000 133 0.0000000 0.0000207 5
17 70723226 70723386 0.0000000 160 0.0000000 0.0000504 2
20 35169593 35169886 0.0000000 293 0.0000001 0.0000373 5
17 78549323 78549371 0.0000000 48 0.0000001 0.0003164 3
3 16216093 16216215 0.0000001 122 0.0000001 0.0002044 4
14 78447480 78447640 0.0000001 160 0.0000001 0.0001737 3
17 149483 149488 0.0000001 5 0.0000002 0.0111041 2
10 135051232 135051351 0.0000006 119 0.0000007 0.0020801 7
12 54070516 54070591 0.0000107 75 0.0000115 0.0546485 4
16 8806689 8806756 0.0003889 67 0.0003889 0.8987147 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_manhattan_DMP_adj.png")

Hg

DMP_Hg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk')

# Unadjusted, N =  326 
# Unadjusted, p<0.05:  37293 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  326 
# Adjusted, p<0.05:  26572 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.213221 
 
# Number of DMRs identified:   4 

DMP_Hg_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
17 46681110 46681401 0.00e+00 291 0.00e+00 0.0000009 6
6 31846768 31847009 0.00e+00 241 0.00e+00 0.0000034 9
10 131843516 131843798 0.00e+00 282 0.00e+00 0.0000112 4
3 42977888 42978026 2.93e-05 138 2.93e-05 0.0802830 4
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, female

DMP_Hg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk')

# Unadjusted, N =  154 
# Unadjusted, p<0.05:  35686 
# Unadjusted, FDR<0.05:  156 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  154 
# Adjusted, p<0.05:  15090 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8796583 
 
# Number of DMRs identified:   3 

DMP_Hg_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
12 47219625 47220092 0e+00 467 0e+00 0.0000001 12
4 165877874 165878136 0e+00 262 0e+00 0.0000008 6
7 27143234 27143478 1e-07 244 1e-07 0.0001227 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, male

DMP_Hg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk')

# Unadjusted, N =  172 
# Unadjusted, p<0.05:  22412 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  172 
# Adjusted, p<0.05:  24091 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.207859 
 
# Number of DMRs identified:   9 

DMP_Hg_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
6 31846768 31847009 0.0000000 241 0.0000000 0.0000000 9
11 18477152 18477534 0.0000000 382 0.0000000 0.0000001 7
11 18433499 18433887 0.0000000 388 0.0000000 0.0000001 5
5 502290 502571 0.0000000 281 0.0000000 0.0000004 3
6 33282735 33283162 0.0000000 427 0.0000000 0.0000011 20
14 104690039 104690244 0.0000000 205 0.0000000 0.0000129 5
1 147737015 147737207 0.0000001 192 0.0000002 0.0002762 4
1 2345151 2345410 0.0000002 259 0.0000002 0.0002468 8
1 117317981 117318133 0.0011583 152 0.0011583 0.9505995 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_manhattan_DMP_adj.png")

Mg

DMP_Mg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  18232 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  15821 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.8746056 
 
# Number of DMRs identified:   5 

DMP_Mg_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
20 3051953 3052345 0.0000000 392 0.0000000 0.0000000 9
6 31543539 31543686 0.0000000 147 0.0000000 0.0000353 8
2 240196768 240196996 0.0000001 228 0.0000001 0.0000921 3
11 368564 368712 0.0000014 148 0.0000017 0.0035951 7
6 10884093 10884140 0.0007239 47 0.0007239 0.9977073 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, female

DMP_Mg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  33977 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  20594 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.079708 
 
# Number of DMRs identified:   2 

DMP_Mg_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
2 240196876 240196996 0.0000008 120 0.0000017 0.0027396 2
6 10884093 10884140 0.0001867 47 0.0001867 0.7913380 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, male

DMP_Mg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  9395 
# Unadjusted, FDR<0.05:  7 
# Unadjusted, pBonf<0.05:  5 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13551 
# Adjusted, FDR<0.05:  3 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8048792 

# Number of identified DMR:  2

DMP_Mg_M_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg13434714 -0.6 (-0.79 ,-0.41) -5.78 0 0.0016633 0.0017 chr12 6936787 LEPREL2
cg18670846 0.84 (0.56 ,1.12) -2.30 0 0.0030248 0.0060 chr2 68917482
cg26708724 0.89 (0.58 ,1.19) 6.72 0 0.0059299 0.0178 chr4 187509785 FAT1

DMRs

chr start end p length fdr sidak nprobe
5 23507449 23507656 0 207 0 6.62e-05 5
17 37123668 37123949 0 281 0 5.24e-05 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_manhattan_DMP_adj.png")

Mn

DMP_Mn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  27983 
# Unadjusted, FDR<0.05:  6 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  37788 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.339163 
 
# Number of DMRs identified:   10 

DMP_Mn_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk_beta')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  34004 
# Unadjusted, FDR<0.05:  2096 
# Unadjusted, pBonf<0.05:  39 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  42632 
# Adjusted, FDR<0.05:  5339 
# Adjusted, pBonf<0.05:  75 
# Adjusted, lambda:  1.240793 
 
# Number of DMRs identified:   121 

DMP_Mn_age7_beta[[3]][DMP_Mn_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg02042823 0.7500762 0.1418274 1.358325

rm(DMP_Mn_age7_beta);gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00808511 0.18 (0.11 ,0.25) 2.86 1.5e-06 0.0441289 0.5737 chr16 52495237 TOX3;TOX3
cg03716590 0.18 (0.11 ,0.25) 5.09 9.0e-07 0.0357372 0.3580 chr7 95435309 DYNC1I1;DYNC1I1;DYNC1I1
cg05613017 0.2 (0.12 ,0.28) 5.33 5.0e-07 0.0310721 0.2156 chr12 65589446 LEMD3;LEMD3
cg09856068 -0.11 (-0.16 ,-0.07) -4.37 8.0e-07 0.0357372 0.3012 chr5 170878246 FGF18
cg11063328 -0.16 (-0.22 ,-0.1) -6.02 6.0e-07 0.0310721 0.2175 chr11 18343203 GTF2H1;HPS5;HPS5;HPS5;GTF2H1
cg13834844 -0.1 (-0.14 ,-0.06) -5.14 1.0e-07 0.0138786 0.0555 chr10 102415320
cg14252211 0.2 (0.13 ,0.26) 5.85 0.0e+00 0.0023306 0.0047 chr1 25919394
cg19407717 0.31 (0.22 ,0.4) 4.03 0.0e+00 0.0000169 0.0000 chr2 1544120 TPO;TPO;TPO;TPO
cg19425870 -0.15 (-0.21 ,-0.09) -6.46 1.0e-06 0.0357372 0.3931 chr11 3876808 STIM1
cg22586726 0.27 (0.16 ,0.38) -0.97 1.3e-06 0.0424978 0.5100 chr10 134150542 LRRC27;LRRC27;LRRC27;LRRC27;LRRC27
cg24196240 0.33 (0.21 ,0.45) 5.25 1.0e-07 0.0114167 0.0343 chr21 36096009 NCRNA00160
cg25101184 0.25 (0.15 ,0.34) 3.38 8.0e-07 0.0357372 0.3286 chr14 56231604 RPL13AP3
cg27095984 -0.19 (-0.26 ,-0.12) 5.27 3.0e-07 0.0216665 0.1083 chr13 21652115

DMRs

chr start end p length fdr sidak nprobe
10 134150488 134150760 0.0000000 272 0.0000000 0.0000000 7
19 21657528 21657756 0.0000000 228 0.0000000 0.0000002 4
16 30572738 30573013 0.0000000 275 0.0000000 0.0000004 5
10 45406680 45406847 0.0000000 167 0.0000000 0.0000545 3
16 73100425 73100510 0.0000000 85 0.0000000 0.0001310 2
11 76839190 76839476 0.0000000 286 0.0000000 0.0000395 4
20 61659979 61660250 0.0000001 271 0.0000001 0.0001260 2
15 91473290 91473386 0.0000226 96 0.0000282 0.0885929 3
10 35484767 35484824 0.0003062 57 0.0003402 0.8798961 3
10 530950 531098 0.0019955 148 0.0019955 0.9951256 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, female

DMP_Mn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  28256 
# Unadjusted, FDR<0.05:  3 
# Unadjusted, pBonf<0.05:  3 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  39831 
# Adjusted, FDR<0.05:  6 
# Adjusted, pBonf<0.05:  2 
# Adjusted, lambda:  1.354546 
 
# Number of DMRs identified:   1

DMP_Mn_F_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_F_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk_beta')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  34431 
# Unadjusted, FDR<0.05:  3379 
# Unadjusted, pBonf<0.05:  42 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  43301 
# Adjusted, FDR<0.05:  7595 
# Adjusted, pBonf<0.05:  69 
# Adjusted, lambda:  1.248445 
 
# Number of DMRs identified:   171 

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg00954161',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg00954161 1.333573 0.6920163 1.975131

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg11161853',c(2:4)]*100
                # logFC        CI.L       CI.R
# cg11161853 0.00902998 -0.05582495 0.07388491

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg23903787',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg23903787 2.035622 0.7851984 3.286046

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg19908812',c(2:4)]*100
                 # logFC       CI.L      CI.R
# cg19908812 -0.03226102 -0.3388754 0.2743534

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg26462130',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg26462130 0.9842899 0.6837261 1.284854

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg08904630',c(2:4)]*100
               # logFC      CI.L      CI.R
# cg08904630 0.4763335 0.3358858 0.6167811

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg22799518',c(2:4)]*100
                # logFC       CI.L       CI.R
# cg22799518 -0.2005144 -0.4265598 0.02553097

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg01744822',c(2:4)]*100
               # logFC      CI.L      CI.R
# cg01744822 -1.662075 -2.293577 -1.030573

DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg15712310',c(2:4)]*100
                # logFC      CI.L        CI.R
# cg15712310 -0.9650864 -1.858607 -0.07156615

rm(DMP_Mn_F_age7_beta);gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg02920176 0.28 (0.17 ,0.38) 5.13 7e-07 0.0478732 0.2859 chr7 36404389 KIAA0895;KIAA0895
cg05613017 0.26 (0.16 ,0.36) 5.32 7e-07 0.0478732 0.2854 chr12 65589446 LEMD3;LEMD3
cg11063328 -0.26 (-0.33 ,-0.18) -6.00 0e+00 0.0003803 0.0005 chr11 18343203 GTF2H1;HPS5;HPS5;HPS5;GTF2H1
cg16675029 -0.11 (-0.15 ,-0.07) -6.42 7e-07 0.0478732 0.2872 chr8 6565876 AGPAT5
cg19425870 -0.25 (-0.32 ,-0.17) -6.45 0e+00 0.0003803 0.0008 chr11 3876808 STIM1
cg22396353 -0.15 (-0.2 ,-0.1) -6.10 1e-07 0.0170936 0.0513 chr22 46692687 GTSE1;GTSE1;CN5H6.4

DMRs

chr start end p length fdr sidak nprobe
6 3849410 3849690 5e-07 280 5e-07 0.0007357 10
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, male

DMP_Mn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  14905 
# Unadjusted, FDR<0.05:  27 
# Unadjusted, pBonf<0.05:  9 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  18986 
# Adjusted, FDR<0.05:  30 
# Adjusted, pBonf<0.05:  13 
# Adjusted, lambda:  0.9800403 
 
# Number of DMRs identified:   14 

DMP_Mn_M_age7[[3]] = NULL

# limma on Beta-values
DMP_Mn_M_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk_beta')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  14417 
# Unadjusted, FDR<0.05:  227 
# Unadjusted, pBonf<0.05:  82 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  18971 
# Adjusted, FDR<0.05:  257 
# Adjusted, pBonf<0.05:  85 
# Adjusted, lambda:  0.9273041 
 
# Number of DMRs identified:   27 

DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg03763518',c(2:4)]*100
               # logFC      CI.L     CI.R
# cg03763518 -3.025927 -4.557014 -1.49484

DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
              # logFC      CI.L     CI.R
# cg02042823 1.815752 0.5050111 3.126493

rm(DMP_Mn_M_age7_beta);gc()

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg03425412 -0.22 (-0.31 ,-0.14) -5.94 1.1e-06 0.0200355 0.4408 chr20 21500337
cg04143120 0.41 (0.27 ,0.55) 6.79 0.0e+00 0.0009703 0.0068 chr11 72968848
cg04885068 0.19 (0.12 ,0.25) 6.47 1.0e-07 0.0034580 0.0386 chr1 9099298 SLC2A5;SLC2A5
cg05041382 -0.12 (-0.17 ,-0.07) -6.39 2.4e-06 0.0357914 0.9313 chr13 50366546 KPNA3
cg05249026 -0.16 (-0.22 ,-0.1) -2.36 3.0e-07 0.0071381 0.1213 chr16 11031524 DEXI
cg06051716 0.36 (0.24 ,0.47) 6.49 0.0e+00 0.0002792 0.0015 chr6 169225783
cg06756211 -0.21 (-0.27 ,-0.14) -6.05 0.0e+00 0.0002792 0.0017 chr1 223936799 CAPN2;CAPN2
cg06883949 -0.12 (-0.17 ,-0.07) -6.47 8.0e-07 0.0151676 0.3034 chr4 1795240 FGFR3;FGFR3;FGFR3
cg08072480 -0.14 (-0.19 ,-0.08) -6.61 2.0e-06 0.0320210 0.7829 chr11 65292666 SCYL1;SCYL1
cg10088075 -0.11 (-0.16 ,-0.07) -6.21 3.8e-06 0.0499734 1.0000 chr16 30407103 ZNF48;ZNF48
cg11480534 0.4 (0.24 ,0.55) 5.84 9.0e-07 0.0173628 0.3646 chr11 62255850 AHNAK
cg11521780 -0.14 (-0.18 ,-0.09) -5.77 0.0e+00 0.0015624 0.0125 chr12 53693949 C12orf10
cg11755803 0.4 (0.24 ,0.56) 5.79 1.7e-06 0.0288393 0.6633 chr12 129000542 TMEM132C
cg12700904 -0.1 (-0.14 ,-0.06) -5.94 2.9e-06 0.0388460 1.0000 chr3 13590720 FBLN2;FBLN2
cg12828656 -0.15 (-0.2 ,-0.1) -0.50 0.0e+00 0.0002792 0.0012 chr5 132577108 FSTL4
cg13834844 -0.15 (-0.22 ,-0.09) -5.13 2.0e-06 0.0320210 0.8005 chr10 102415320
cg13848566 -0.17 (-0.22 ,-0.11) -6.36 2.0e-07 0.0041615 0.0624 chr9 89561175 GAS1
cg14149680 -0.29 (-0.38 ,-0.2) -6.35 0.0e+00 0.0001372 0.0004 chr11 2187632 TH;TH;TH
cg16560774 -0.17 (-0.22 ,-0.11) -6.46 0.0e+00 0.0018682 0.0168 chr17 79373381 BAHCC1
cg19407717 0.5 (0.35 ,0.64) 4.03 0.0e+00 0.0000364 0.0001 chr2 1544120 TPO;TPO;TPO;TPO
cg19511862 -0.1 (-0.14 ,-0.06) -6.26 5.0e-07 0.0106449 0.2023 chr12 125478458 BRI3BP
cg19641404 -0.11 (-0.16 ,-0.07) -5.87 2.5e-06 0.0357914 0.9762 chr2 232826272 DIS3L2
cg20414082 0.26 (0.16 ,0.36) 3.20 4.0e-07 0.0085706 0.1543 chr1 203002593
cg20504533 -0.22 (-0.28 ,-0.15) -5.85 0.0e+00 0.0000364 0.0001 chr17 15848253 ADORA2B;ADORA2B
cg22563312 -0.17 (-0.22 ,-0.11) -6.27 1.0e-07 0.0034580 0.0450 chr5 179334739 TBC1D9B;TBC1D9B
cg22702772 -0.15 (-0.2 ,-0.1) -6.69 1.0e-07 0.0034580 0.0430 chr3 48699012 CELSR3
cg24196240 0.42 (0.27 ,0.56) 5.27 2.0e-07 0.0041615 0.0617 chr21 36096009 NCRNA00160
cg24948962 -0.22 (-0.29 ,-0.14) -5.44 1.0e-07 0.0034580 0.0385 chr18 2906032 EMILIN2
cg25152909 0.43 (0.27 ,0.58) 6.08 2.0e-07 0.0043902 0.0702 chr5 172566090 C5orf41
cg25466588 -0.09 (-0.13 ,-0.06) -5.90 2.5e-06 0.0357914 1.0000 chr3 23958904 NKIRAS1;RPL15

DMRs

chr start end p length fdr sidak nprobe
1 161008461 161008977 0.0000000 516 0.0000000 0.0000000 8
19 21657528 21658001 0.0000000 473 0.0000000 0.0000000 5
19 10736005 10736117 0.0000000 112 0.0000000 0.0000055 5
20 5485244 5485511 0.0000000 267 0.0000000 0.0000036 6
4 79971176 79971432 0.0000000 256 0.0000000 0.0000079 4
20 35169593 35169886 0.0000000 293 0.0000000 0.0000081 5
1 9099280 9099462 0.0000001 182 0.0000002 0.0001641 3
6 26018002 26018185 0.0000001 183 0.0000002 0.0002514 6
16 30572738 30573013 0.0000001 275 0.0000002 0.0001883 5
3 39543966 39544192 0.0000032 226 0.0000045 0.0055785 2
15 91473090 91473365 0.0000066 275 0.0000084 0.0094606 4
19 12444612 12444741 0.0000102 129 0.0000119 0.0307855 5
6 37616597 37616686 0.0000933 89 0.0001005 0.3386856 2
2 3642628 3642634 0.0032946 6 0.0032946 1.0000000 2
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_manhattan_DMP_adj.png")

Pb

DMP_Pb_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  13157 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  19598 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  1.056675 

# Number of DMRs identified:   6 

DMP_Pb_age7[[3]] = NULL

# limma on Beta-values
DMP_Pb_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk_beta')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  13578 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20646 
# Adjusted, FDR<0.05:  1 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  1.092762 
 
# Number of DMRs identified:   6 

DMP_Pb_age7_beta[[3]][DMP_Pb_age7_beta[[3]]$cpg == 'cg20608990',c(2:4)]*100
               # logFC      CI.L       CI.R
# cg20608990 -1.564971 -2.725569 -0.4043731

rm(DMP_Pb_age7_beta);gc()

FDR-sgnificant DMPs

x
NA

DMRs

chr start end p length fdr sidak nprobe
10 135051021 135051581 0e+00 560 0e+00 0.0000000 11
22 45704901 45705265 0e+00 364 0e+00 0.0000000 7
22 19746155 19746368 0e+00 213 0e+00 0.0000225 3
3 130745441 130745685 0e+00 244 0e+00 0.0000389 10
7 155283139 155283424 0e+00 285 1e-07 0.0000621 3
14 104690039 104690244 1e-07 205 1e-07 0.0002063 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, female

DMP_Pb_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  10571 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  12151 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.7522295 
 
# Number of identified DMR:  0

DMP_Pb_F_age7[[3]] = NULL
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, male

DMP_Pb_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  18362 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14153 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9440498 
 
# Number of DMRs identified:   4 

DMP_Pb_M_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
6 33084769 33084985 0 216 0 1.00e-07 11
1 68512649 68513063 0 414 0 3.00e-07 7
6 31148369 31148748 0 379 0 2.70e-06 13
22 45704987 45705265 0 278 0 6.82e-05 5
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_manhattan_DMP_adj.png")

Se

DMP_Se_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  17270 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  20324 
# Adjusted, FDR<0.05:  4 
# Adjusted, pBonf<0.05:  1 
# Adjusted, lambda:  0.9736407 
 
# Number of DMRs identified:   3 

DMP_Se_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg08760128 0.2 (0.13 ,0.28) 6.73 4e-07 0.0460845 0.1487 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1
cg10145926 0.55 (0.35 ,0.75) 5.31 1e-07 0.0286748 0.0573 chr14 95875792 C14orf139
cg13434714 -0.42 (-0.57 ,-0.28) -5.77 0e+00 0.0077289 0.0077 chr12 6936787 LEPREL2
cg26708724 0.59 (0.36 ,0.81) 6.73 5e-07 0.0460845 0.1843 chr4 187509785 FAT1

DMRs

chr start end p length fdr sidak nprobe
17 47091977 47092178 0 201 0 4.00e-06 4
19 50194119 50194252 0 133 0 1.57e-05 5
6 49681177 49681391 0 214 0 2.89e-05 7
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_manhattan_DMP_adj.png")

Se, female

DMP_Se_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  26254 
# Unadjusted, FDR<0.05:  9 
# Unadjusted, pBonf<0.05:  2 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  16049 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9296273 
 
# Number of DMRs identified:   3 

DMP_Se_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
10 38146245 38146671 0 426 0 4.00e-07 9
6 49681177 49681391 0 214 0 1.00e-06 7
10 38299241 38299574 0 333 0 1.83e-05 9
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_manhattan_DMP_adj.png")

Se, male

DMP_Se_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  15593 
# Unadjusted, FDR<0.05:  42 
# Unadjusted, pBonf<0.05:  12 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  13808 
# Adjusted, FDR<0.05:  20 
# Adjusted, pBonf<0.05:  6 
# Adjusted, lambda:  0.7972324 
 
# Number of DMRs identified:   3 

DMP_Se_M_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00326183 0.4 (0.24 ,0.56) 2.20 1.8e-06 0.0389133 0.7004 chr2 241808259 AGXT;AGXT
cg00908120 0.6 (0.36 ,0.83) 6.29 1.1e-06 0.0299539 0.4194 chr16 72872925 ZFHX3;ZFHX3
cg01007589 0.77 (0.47 ,1.07) 4.79 1.4e-06 0.0359853 0.5398 chr19 49894178 CCDC155
cg01588060 -0.27 (-0.38 ,-0.17) -5.90 8.0e-07 0.0259001 0.3108 chr6 2245749 GMDS;GMDS
cg04692924 -0.59 (-0.8 ,-0.38) -6.58 1.0e-07 0.0071719 0.0547 chr1 161720042 DUSP12
cg05051957 -0.66 (-0.88 ,-0.44) -5.61 0.0e+00 0.0015014 0.0046 chr8 141522459 CHRAC1;CHRAC1
cg06723863 -0.34 (-0.47 ,-0.22) -5.99 1.0e-07 0.0071719 0.0574 chr16 68270129 ESRP2;ESRP2
cg07599133 -0.34 (-0.48 ,-0.21) -5.96 1.8e-06 0.0389133 0.6939 chr19 35068628 LOC643719
cg11443888 0.28 (0.17 ,0.39) 2.36 1.9e-06 0.0392822 0.7464 chr6 44244590 TMEM151B
cg11608893 0.84 (0.55 ,1.12) 6.08 1.0e-07 0.0039836 0.0199 chr6 32059542 TNXB
cg12243007 0.44 (0.27 ,0.61) -0.77 1.0e-06 0.0289023 0.3757 chr17 184018 RPH3AL
cg12897502 -0.84 (-1.16 ,-0.52) 6.10 6.0e-07 0.0204295 0.2247 chr8 67425316 C8orf46
cg13434714 -0.63 (-0.81 ,-0.45) -5.78 0.0e+00 0.0000186 0.0000 chr12 6936787 LEPREL2
cg16656826 0.29 (0.18 ,0.41) 0.14 1.5e-06 0.0376409 0.6023 chr5 159343871 ADRA1B;ADRA1B
cg18377660 0.71 (0.45 ,0.97) 5.65 2.0e-07 0.0089756 0.0808 chr1 57535755 DAB1
cg19005275 0.59 (0.37 ,0.81) 4.29 4.0e-07 0.0162778 0.1628 chr12 113588263 CCDC42B
cg21373263 0.82 (0.55 ,1.1) 3.29 0.0e+00 0.0015014 0.0060 chr10 126751982 CTBP2;CTBP2
cg25067702 -0.64 (-0.87 ,-0.41) -6.40 1.0e-07 0.0065970 0.0396 chr17 70723227 SLC39A11;SLC39A11
cg26342676 0.61 (0.37 ,0.86) 4.56 2.3e-06 0.0454735 0.9095 chr14 37639757 SLC25A21;SLC25A21;LOC100129794
cg26708724 1.01 (0.73 ,1.3) 6.72 0.0e+00 0.0000174 0.0000 chr4 187509785 FAT1

DMRs

chr start end p length fdr sidak nprobe
17 70723226 70723386 0e+00 160 0e+00 0.0000001 2
4 24796918 24797176 0e+00 258 0e+00 0.0000241 6
10 121578383 121578639 1e-07 256 1e-07 0.0001184 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_manhattan_DMP_adj.png")

Zn

DMP_Zn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk')

# Unadjusted, N =  333 
# Unadjusted, p<0.05:  12854 
# Unadjusted, FDR<0.05:  1 
# Unadjusted, pBonf<0.05:  1 
 
# Adjusted, N =  333 
# Adjusted, p<0.05:  23322 
# Adjusted, FDR<0.05:  13 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  1.103711 
 
# Number of DMRs identified:   13

DMP_Zn_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00082497 -0.28 (-0.38 ,-0.18) -5.32 1.0e-07 0.0122297 0.0337 chr1 32802133 MARCKSL1
cg00908120 0.49 (0.31 ,0.67) 6.26 3.0e-07 0.0170276 0.1166 chr16 72872925 ZFHX3;ZFHX3
cg04015129 0.65 (0.4 ,0.91) 4.28 8.0e-07 0.0307007 0.3136 chr10 1058036 GTPBP4
cg05573434 0.41 (0.26 ,0.57) -3.15 3.0e-07 0.0170276 0.1192 chr4 7648540 SORCS2
cg06723863 -0.25 (-0.35 ,-0.15) -5.98 1.6e-06 0.0495322 0.6439 chr16 68270129 ESRP2;ESRP2
cg08459368 0.59 (0.38 ,0.81) 2.65 1.0e-07 0.0122297 0.0395 chr11 61974948 SCGB2A1
cg10653573 0.82 (0.5 ,1.14) 5.43 7.0e-07 0.0307007 0.2910 chr8 141347297 TRAPPC9;TRAPPC9
cg13434714 -0.49 (-0.64 ,-0.33) -5.77 0.0e+00 0.0012560 0.0013 chr12 6936787 LEPREL2
cg15528091 -0.31 (-0.43 ,-0.19) -6.36 9.0e-07 0.0307007 0.3391 chr19 18119069 ARRDC2;ARRDC2;ARRDC2
cg16496814 0.21 (0.13 ,0.3) 5.21 6.0e-07 0.0299711 0.2398 chr11 9778721
cg19011752 0.25 (0.15 ,0.34) -2.54 9.0e-07 0.0307007 0.3684 chr21 45772638 TRPM2
cg23477849 0.26 (0.16 ,0.36) 4.88 2.0e-07 0.0122297 0.0600 chr19 5698492 LONP1
cg25954729 -0.22 (-0.29 ,-0.14) -6.34 2.0e-07 0.0122297 0.0611 chr11 66610784 RCE1;C11orf80;RCE1

DMRs

chr start end p length fdr sidak nprobe
12 54070516 54070610 0.0000000 94 0.0000000 0.0000053 5
19 18118799 18119069 0.0000000 270 0.0000000 0.0000104 3
10 124638975 124639260 0.0000000 285 0.0000001 0.0000244 12
6 32063990 32064258 0.0000001 268 0.0000002 0.0000840 12
4 7648539 7648627 0.0000001 88 0.0000002 0.0003269 2
8 41655672 41655894 0.0000001 222 0.0000002 0.0002414 4
6 41168800 41169049 0.0000001 249 0.0000002 0.0002270 6
17 1395863 1396123 0.0000002 260 0.0000002 0.0002710 5
12 54385274 54385526 0.0000002 252 0.0000002 0.0002813 4
17 79503641 79503877 0.0000002 236 0.0000002 0.0003092 4
22 45704987 45705042 0.0000002 55 0.0000003 0.0015642 4
20 25129506 25129562 0.0000016 56 0.0000017 0.0113002 5
20 35169593 35169846 0.0004394 253 0.0004394 0.4960606 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, female

DMP_Zn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk')

# Unadjusted, N =  158 
# Unadjusted, p<0.05:  12830 
# Unadjusted, FDR<0.05:  0 
# Unadjusted, pBonf<0.05:  0 
 
# Adjusted, N =  158 
# Adjusted, p<0.05:  17367 
# Adjusted, FDR<0.05:  0 
# Adjusted, pBonf<0.05:  0 
# Adjusted, lambda:  0.9501586 

# Number of DMRs identified:   1 

DMP_Zn_F_age7[[3]] = NULL

DMRs

chr start end p length fdr sidak nprobe
11 73357018 73357396 0 378 0 0 8
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, male

DMP_Zn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk')

# Unadjusted, N =  175 
# Unadjusted, p<0.05:  16787 
# Unadjusted, FDR<0.05:  36 
# Unadjusted, pBonf<0.05:  8 
 
# Adjusted, N =  175 
# Adjusted, p<0.05:  14614 
# Adjusted, FDR<0.05:  37 
# Adjusted, pBonf<0.05:  3 
# Adjusted, lambda:  0.8610523 
 
# Number of DMRs identified:   16 

DMP_Zn_M_age7[[3]] = NULL

FDR-significant DMPs

logFC_CI AveExpr P.Value adj.P.Val adj.P.Val.bonf chr pos gene
cg00908120 0.79 (0.52 ,1.06) 6.29 0.0e+00 0.0059562 0.0162 chr16 72872925 ZFHX3;ZFHX3
cg01007589 0.92 (0.56 ,1.28) 4.79 1.1e-06 0.0188947 0.4346 chr19 49894178 CCDC155
cg01063965 -0.27 (-0.38 ,-0.16) -6.44 4.3e-06 0.0462438 1.0000 chr11 695461 TMEM80;TMEM80;DEAF1;DEAF1
cg01447660 0.42 (0.25 ,0.59) -0.92 2.9e-06 0.0363415 1.0000 chr2 69152678
cg02196294 -0.29 (-0.41 ,-0.17) -5.41 4.0e-06 0.0443654 1.0000 chr6 39197260 KCNK5
cg02490920 0.39 (0.24 ,0.54) 1.34 1.1e-06 0.0188947 0.4228 chr3 50304406 SEMA3B;SEMA3B
cg02711608 0.54 (0.34 ,0.74) -2.09 3.0e-07 0.0124570 0.1004 chr19 47287964 SLC1A5;SLC1A5;SLC1A5;SLC1A5
cg02968175 0.33 (0.2 ,0.45) 5.76 7.0e-07 0.0136814 0.2736 chr16 4690020 MGRN1;MGRN1;MGRN1;MGRN1
cg03352332 0.89 (0.55 ,1.22) 5.54 5.0e-07 0.0124570 0.1869 chr3 186360953 FETUB
cg04015129 0.86 (0.55 ,1.18) 4.27 3.0e-07 0.0124570 0.0993 chr10 1058036 GTPBP4
cg04374006 0.27 (0.16 ,0.37) -0.27 2.3e-06 0.0311662 0.9038 chr19 33556395 RHPN2
cg04406071 -0.32 (-0.45 ,-0.2) -6.07 7.0e-07 0.0136814 0.2633 chr17 59489784 C17orf82
cg04692924 -0.66 (-0.91 ,-0.41) -6.58 8.0e-07 0.0148121 0.3111 chr1 161720042 DUSP12
cg05051957 -0.65 (-0.92 ,-0.39) -5.61 3.1e-06 0.0382640 1.0000 chr8 141522459 CHRAC1;CHRAC1
cg06723863 -0.36 (-0.51 ,-0.21) -5.99 3.3e-06 0.0382640 1.0000 chr16 68270129 ESRP2;ESRP2
cg07380021 -0.66 (-0.91 ,-0.41) -5.43 4.0e-07 0.0124570 0.1536 chr1 206755252 RASSF5;RASSF5;RASSF5
cg08760128 0.36 (0.23 ,0.49) 6.73 1.0e-07 0.0124570 0.0590 chr16 4723507 MGRN1;MGRN1;MGRN1;MGRN1
cg10266648 1.03 (0.62 ,1.44) 5.98 1.8e-06 0.0268172 0.6972 chr2 106560529
cg10653573 1.41 (0.89 ,1.93) 5.37 3.0e-07 0.0124570 0.1021 chr8 141347297 TRAPPC9;TRAPPC9
cg10923018 0.31 (0.18 ,0.43) 2.73 3.2e-06 0.0382640 1.0000 chr6 31743769 C6orf27
cg11761483 -0.72 (-0.99 ,-0.45) -5.60 4.0e-07 0.0124570 0.1584 chr17 70723386 SLC39A11;SLC39A11
cg13434714 -0.83 (-1.04 ,-0.63) -5.78 0.0e+00 0.0000001 0.0000 chr12 6936787 LEPREL2
cg14230280 1.23 (0.74 ,1.72) 4.28 1.9e-06 0.0274435 0.7684 chr9 132502800 PTGES
cg16496814 0.32 (0.2 ,0.44) 5.22 4.0e-07 0.0124570 0.1617 chr11 9778721
cg16656826 0.35 (0.21 ,0.48) 0.14 1.9e-06 0.0273935 0.7396 chr5 159343871 ADRA1B;ADRA1B
cg18037826 0.41 (0.26 ,0.57) 4.29 6.0e-07 0.0136814 0.2473 chr12 109273835 DAO
cg19005275 0.75 (0.49 ,1.01) 4.29 0.0e+00 0.0059562 0.0179 chr12 113588263 CCDC42B
cg19532212 0.75 (0.47 ,1.03) 4.42 3.0e-07 0.0124570 0.1355 chr17 56769430 TEX14;RAD51C;TEX14;RAD51C
cg21373263 0.88 (0.55 ,1.21) 3.29 4.0e-07 0.0124570 0.1769 chr10 126751982 CTBP2;CTBP2
cg22240394 1.22 (0.76 ,1.67) 6.82 5.0e-07 0.0124570 0.1825 chr3 186211630
cg22413938 -0.39 (-0.55 ,-0.23) -4.56 2.5e-06 0.0328489 0.9855 chr14 78447481
cg23477849 0.38 (0.23 ,0.53) 4.90 1.6e-06 0.0255962 0.6399 chr19 5698492 LONP1
cg23601521 0.8 (0.49 ,1.1) 4.87 6.0e-07 0.0136814 0.2553 chr2 50275179 NRXN1;NRXN1;NRXN1
cg25954729 -0.3 (-0.41 ,-0.19) -6.37 4.0e-07 0.0124570 0.1703 chr11 66610784 RCE1;C11orf80;RCE1
cg26608798 0.4 (0.24 ,0.56) 0.58 1.6e-06 0.0255962 0.6283 chr16 33853544
cg26708724 0.94 (0.58 ,1.29) 6.72 6.0e-07 0.0136814 0.2306 chr4 187509785 FAT1
cg27503275 0.47 (0.28 ,0.66) 4.12 3.5e-06 0.0389303 1.0000 chr6 3880016

DMRs

chr start end p length fdr sidak nprobe
17 70723226 70723386 0.0000000 160 0.0000000 0.0000015 2
10 121578136 121578639 0.0000000 503 0.0000000 0.0000016 4
4 24796918 24797176 0.0000000 258 0.0000000 0.0000052 6
14 78447480 78447640 0.0000000 160 0.0000000 0.0000104 3
19 50194119 50194252 0.0000000 133 0.0000000 0.0000187 5
4 186732836 186733060 0.0000000 224 0.0000000 0.0000223 7
14 76734326 76734605 0.0000000 279 0.0000000 0.0000293 5
21 45773781 45773997 0.0000000 216 0.0000001 0.0000492 2
5 135416204 135416613 0.0000000 409 0.0000001 0.0000444 9
11 63679431 63679637 0.0000001 206 0.0000001 0.0001629 2
20 62716331 62716606 0.0000001 275 0.0000002 0.0001988 4
17 78549323 78549371 0.0000002 48 0.0000002 0.0013191 3
5 1868136 1868357 0.0000004 221 0.0000005 0.0007748 4
22 45704987 45705042 0.0000016 55 0.0000018 0.0110616 4
5 176755392 176755449 0.0000113 57 0.0000120 0.0749153 2
2 88583556 88583805 0.0001352 249 0.0001352 0.1927662 3
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_manhattan_DMP_adj.png")